A "Do-It-Yourself" phenotyping system: measuring growth and morphology throughout the diel cycle in rosette shaped plantshttp://hdl.handle.net/10283/29222018-12-19T09:57:52Z2018-12-19T09:57:52ZSoftware - executable for Windows (beta)http://hdl.handle.net/10283/29582017-12-03T16:04:26Z2017-11-24T14:52:27ZSoftware - executable for Windows (beta)
2017-11-24T14:52:27ZSoftware - source code (beta)http://hdl.handle.net/10283/29572017-11-24T15:15:33Z2017-11-24T14:52:17ZSoftware - source code (beta)
2017-11-24T14:52:17ZManualhttp://hdl.handle.net/10283/29562017-11-24T15:15:33Z2017-11-24T14:52:08ZManual
Improvements in high-throughput phenotyping technologies are rapidly expanding the scope and capacity of plant biology studies to measure growth traits. Nevertheless, the costs of commercial phenotyping equipment and infrastructure remain prohibitively expensive for wide-scale uptake, while academic solutions can require significant local expertise. Here a low-cost methodology for plant biologists to build their own phenotyping system for quantifying growth rates and phenotypic characteristics of Arabidopsis thaliana rosettes throughout the diel cycle is presented. The group constructed an image capture system consisting of a near infra-red (NIR, 940 nm) LED panel with a mounted Raspberry PI NoIR camera and developed a MatLab-based software module (iDIEL Plant) to characterise rosette expansion. The software was able to accurately segment and characterise multiple rosettes within an image, regardless of plant arrangement or genotype, and batch process image sets. To further validate the system, wild-type Arabidopsis plants (Col-0) and two mutant lines with reduced Rubisco contents, pale leaves and slow growth phenotypes (1a3b and 1a2b) were grown on a single plant tray. Plants were imaged from 9 to 24 days after germination every 20 minutes throughout the 24 hour light-dark growth cycle (i.e. the diel cycle). The resulting dataset provided a dynamic and uninterrupted characterisation of differences in rosette growth and expansion rates over time for the three lines tested. The methodology offers a straightforward solution for setting up automated, scalable and low-cost phenotyping facilities in a wide range of lab environments that could greatly increase the processing power and scalability of Arabidopsis soil growth experiments. iDIEL Plant software and CAD files for image capture system (ICS).
2017-11-24T14:52:08ZImage - Day 19http://hdl.handle.net/10283/29552017-12-03T16:04:27Z2017-11-24T14:51:57ZImage - Day 19
Improvements in high-throughput phenotyping technologies are rapidly expanding the scope and capacity of plant biology studies to measure growth traits. Nevertheless, the costs of commercial phenotyping equipment and infrastructure remain prohibitively expensive for wide-scale uptake, while academic solutions can require significant local expertise. Here a low-cost methodology for plant biologists to build their own phenotyping system for quantifying growth rates and phenotypic characteristics of Arabidopsis thaliana rosettes throughout the diel cycle is presented. The group constructed an image capture system consisting of a near infra-red (NIR, 940 nm) LED panel with a mounted Raspberry PI NoIR camera and developed a MatLab-based software module (iDIEL Plant) to characterise rosette expansion. The software was able to accurately segment and characterise multiple rosettes within an image, regardless of plant arrangement or genotype, and batch process image sets. To further validate the system, wild-type Arabidopsis plants (Col-0) and two mutant lines with reduced Rubisco contents, pale leaves and slow growth phenotypes (1a3b and 1a2b) were grown on a single plant tray. Plants were imaged from 9 to 24 days after germination every 20 minutes throughout the 24 hour light-dark growth cycle (i.e. the diel cycle). The resulting dataset provided a dynamic and uninterrupted characterisation of differences in rosette growth and expansion rates over time for the three lines tested. The methodology offers a straightforward solution for setting up automated, scalable and low-cost phenotyping facilities in a wide range of lab environments that could greatly increase the processing power and scalability of Arabidopsis soil growth experiments. iDIEL Plant software and CAD files for image capture system (ICS).
2017-11-24T14:51:57ZImages - Night 18-19http://hdl.handle.net/10283/29542017-12-03T16:04:43Z2017-11-24T14:51:45ZImages - Night 18-19
Improvements in high-throughput phenotyping technologies are rapidly expanding the scope and capacity of plant biology studies to measure growth traits. Nevertheless, the costs of commercial phenotyping equipment and infrastructure remain prohibitively expensive for wide-scale uptake, while academic solutions can require significant local expertise. Here a low-cost methodology for plant biologists to build their own phenotyping system for quantifying growth rates and phenotypic characteristics of Arabidopsis thaliana rosettes throughout the diel cycle is presented. The group constructed an image capture system consisting of a near infra-red (NIR, 940 nm) LED panel with a mounted Raspberry PI NoIR camera and developed a MatLab-based software module (iDIEL Plant) to characterise rosette expansion. The software was able to accurately segment and characterise multiple rosettes within an image, regardless of plant arrangement or genotype, and batch process image sets. To further validate the system, wild-type Arabidopsis plants (Col-0) and two mutant lines with reduced Rubisco contents, pale leaves and slow growth phenotypes (1a3b and 1a2b) were grown on a single plant tray. Plants were imaged from 9 to 24 days after germination every 20 minutes throughout the 24 hour light-dark growth cycle (i.e. the diel cycle). The resulting dataset provided a dynamic and uninterrupted characterisation of differences in rosette growth and expansion rates over time for the three lines tested. The methodology offers a straightforward solution for setting up automated, scalable and low-cost phenotyping facilities in a wide range of lab environments that could greatly increase the processing power and scalability of Arabidopsis soil growth experiments. iDIEL Plant software and CAD files for image capture system (ICS).
2017-11-24T14:51:45ZImages - Day 18http://hdl.handle.net/10283/29532017-12-03T16:05:00Z2017-11-24T14:51:16ZImages - Day 18
Test images to accompany manual.
2017-11-24T14:51:16ZCAD files for constructing the image capture systemhttp://hdl.handle.net/10283/29252017-11-24T11:10:06Z2017-10-17T09:37:25ZCAD files for constructing the image capture system
Improvements in high-throughput phenotyping technologies are rapidly expanding the scope and capacity of plant biology studies to measure growth traits. Nevertheless, the costs of commercial phenotyping equipment and infrastructure remain prohibitively expensive for wide-scale uptake, while academic solutions can require significant local expertise. Here a low-cost methodology for plant biologists to build their own phenotyping system for quantifying growth rates and phenotypic characteristics of Arabidopsis thaliana rosettes throughout the diel cycle is presented. The group constructed an image capture system consisting of a near infra-red (NIR, 940 nm) LED panel with a mounted Raspberry PI NoIR camera and developed a MatLab-based software module (iDIEL Plant) to characterise rosette expansion. The software was able to accurately segment and characterise multiple rosettes within an image, regardless of plant arrangement or genotype, and batch process image sets. To further validate the system, wild-type Arabidopsis plants (Col-0) and two mutant lines with reduced Rubisco contents, pale leaves and slow growth phenotypes (1a3b and 1a2b) were grown on a single plant tray. Plants were imaged from 9 to 24 days after germination every 20 minutes throughout the 24 hour light-dark growth cycle (i.e. the diel cycle). The resulting dataset provided a dynamic and uninterrupted characterisation of differences in rosette growth and expansion rates over time for the three lines tested. The methodology offers a straightforward solution for setting up automated, scalable and low-cost phenotyping facilities in a wide range of lab environments that could greatly increase the processing power and scalability of Arabidopsis soil growth experiments.
iDIEL Plant software and CAD files for image capture system (ICS).
2017-10-17T09:37:25Z